How do I combine 2D and 3D animation together?
Combining video images with 3D generated imagery is possible as long as the video in question is encoded using a format supported by blender.

Blender has no support for Flash so the images would need to be transcoded first using a different program.

Likewise. Blender cannot export video on Flash format. You would need to render first on a video format (or image sequence) and encode into Flash with a different program.